ld_prune prunes SNPs based on linkage disequilibrium using SNPRelate and SeqArray packages
ld_prune.Rdld_prune prunes SNPs based on linkage disequilibrium using SNPRelate and SeqArray packages
Usage
ld_prune(
vcf,
out_name,
out_format,
nodes = 1,
ld.threshold = 0.6,
slide.max.n = 100,
maf = 0.05,
seed = 1234,
method = c("corr"),
save_output = TRUE
)Arguments
- vcf
is the path to the vcf file containing all SNPs
- out_name
prefix name of output files (will append with param settings)
- out_format
output file format ("plink" will produce ped and map files while "vcf" will produce a vcf and a GDS)
- nodes
is the number of parallel processors (numeric)
- ld.threshold
is the threshold for LD pruning (numeric; 0 - 1; defaults to 0.6)
- slide.max.n
is the maximum number of SNPs in a sliding window (numeric; defaults to 100)
- maf
is the minor allele frequency cutoff (numeric; defaults to 0.05)
- seed
is the random starting seed (defaults to 1234)
- method
is the LD threshold method; default to corr which is r2 correlation coefficient
- save_output
if TRUE, saves SNP GDS and ped (plink) files with retained SNPs in new directory; if FALSE returns object (defaults to TRUE)